Bio

Bio


I graduated with a Bachelor of Science in Elecrical & Electronics Engineering from Boğaziçi University, Istanbul, Turkey and got my M.S. and Ph.D. degrees in Electical Engineering at Stanford University under the supervision of Dr. Roland Bammer. Currently, I am working as a research associate in the department of Radiology at Stanford University. My primary research interest is the detection and correction of patient motion during magnetic resonance imaging experiments usıng an optical tracking system (i.e., a camera) whıch is installed inside the MR scanner bore. My eventual purpose is to implement this motion tracking system in a clinical setting, which will improve the MR image quality especially for certain patient populations (stroke patients, elderly and children) and will eliminate the need of anesthesia in pediatric population. I also worked on improving the data quality for diffusion-weighted and diffusion-tensor imaging via advanced reconstruction routines, and examined the benefits of such methods on fiber tractography.

Education & Certifications


  • Ph.D., Stanford University, Electrical Engineering (2010)
  • M.S., Stanford University, Electrical Engineering (2005)
  • B.S, Bogazici University, Istanbul, Turkey, Electrical & Electronics Engineering (2003)

Publications

All Publications


  • Trade-off between angular and spatial resolutions in in vivo fiber tractography. NeuroImage Vos, S. B., Aksoy, M., Han, Z., Holdsworth, S. J., Maclaren, J., Viergever, M. A., Leemans, A., Bammer, R. 2016; 129: 117-132

    Abstract

    Tractography is becoming an increasingly popular method to reconstruct white matter connections in vivo. The diffusion MRI data that tractography is based on requires a high angular resolution to resolve crossing fibers whereas high spatial resolution is required to distinguish kissing from crossing fibers. However, scan time increases with increasing spatial and angular resolutions, which can become infeasible in clinical settings. Here we investigated the trade-off between spatial and angular resolutions to determine which of these factors is most worth investing scan time in. We created a unique diffusion MRI dataset with 1.0mm isotropic resolution and a high angular resolution (100 directions) using an advanced 3D diffusion-weighted multi-slab EPI acquisition. This dataset was reconstructed to create subsets of lower angular (75, 50, and 25 directions) and lower spatial (1.5, 2.0, and 2.5mm) resolution. Using all subsets, we investigated the effects of angular and spatial resolutions in three fiber bundles-the corticospinal tract, arcuate fasciculus and corpus callosum-by analyzing the volumetric bundle overlap and anatomical correspondence between tracts. Our results indicate that the subsets of 25 and 50 directions provided inferior tract reconstructions compared with the datasets with 75 and 100 directions. Datasets with spatial resolutions of 1.0, 1.5, and 2.0mm were comparable, while the lowest resolution (2.5mm) datasets had discernible inferior quality. In conclusion, we found that angular resolution appeared to be more influential than spatial resolution in improving tractography results. Spatial resolutions higher than 2.0mm only appear to benefit multi-fiber tractography methods if this is not at the cost of decreased angular resolution.

    View details for DOI 10.1016/j.neuroimage.2016.01.011

    View details for PubMedID 26774615

  • Contact-free physiological monitoring using a markerless optical system MAGNETIC RESONANCE IN MEDICINE Maclaren, J., Aksoy, M., Bammer, R. 2015; 74 (2): 571-577

    Abstract

    Physiological noise remains a major problem in MRI, particularly at higher imaging resolutions and field strengths. The aim of this work was to investigate the feasibility of using an MR-compatible in-bore camera system to perform contactless monitoring of cardiac and respiratory information during MRI of human subjects.An MR-compatible camera was mounted on an eight-channel head coil. Video data of the skin was processed offline to derive cardiac and respiratory signals from the pixel signal intensity and from head motion in the patient head-feet direction. These signals were then compared with data acquired simultaneously from the pulse oximeter and the respiratory belt.The cardiac signal computed using the average image pixel intensity closely resembled the signal obtained using the pulse oximeter. Trigger intervals obtained from both systems matched to within 50 ms (one standard deviation). The respiratory signal computed from small in-plane movements closely matched the signal obtained from the respiratory belt. Simultaneous MR imaging did not appear to have an effect on the physiological signals acquired by means of the contact-free monitoring system.Contact-free monitoring of human subjects to obtain cardiac and respiratory information is feasible using a small camera and light emitting diode mounted on the head coil of an MRI scanner. Magn Reson Med 74:571-577, 2015. © 2015 Wiley Periodicals, Inc.

    View details for DOI 10.1002/mrm.25781

    View details for Web of Science ID 000358607700034

    View details for PubMedID 25982242

  • Effect of Number of Acquisitions in Diffusion Tensor Imaging of the Pediatric Brain: Optimizing Scan Time and Diagnostic Experience JOURNAL OF NEUROIMAGING Soman, S., Holdsworth, S. J., Skare, S., Andre, J. B., Van, A. T., Aksoy, M., Bammer, R., Rosenberg, J., Barnes, P. D., Yeom, K. W. 2015; 25 (2): 296-302

    Abstract

    Diffusion tensor imaging (DTI) is useful for multiple clinical applications, but its routine implementation for children may be difficult due to long scan times. This study evaluates the impact of decreasing the number of DTI acquisitions (NEX) on interpretability of pediatric brain DTI.15 children with MRI-visible neuropathologies were imaged at 3T using our motion-corrected, parallel imaging- accelerated DT-EPI technique with 3 NEX (scan time 8.25 min). Using these acquisitions, NEX = 1 (scan time 2.75 min) and NEX = 2 (scan time 5.5 min) images were simulated. Two neuroradiologists scored diffusion-weighted images (DWI), apparent diffusion coefficient (ADC), fractional anisotropy (FA), and first eigenvector color-encoded (EV) images from each NEX for perceived SNR, lesion conspicuity and clinical confidence. ROI FA/ADC and image SNR values were also compared across NEX.NEX = 2 perceived SNR, lesion conspicuity, and clinical confidence were not inferior to NEX = 3 images. NEX = 1 images showed comparable lesion conspicuity and clinical confidence as NEX = 3, but inferior perceived SNR. FA and ADC ROI measurements demonstrated no significant difference across NEX. The greatest SNR increase was seen between NEX = 1 and NEX = 2.Reducing NEX to shorten imaging time may impact clinical utility in a manner that does not directly correspond with SNR changes.

    View details for DOI 10.1111/jon.12093

    View details for Web of Science ID 000351306000020

  • Real-Time Correction of Rigid Body Motion-Induced Phase Errors for Diffusion-Weighted Steady-State Free Precession Imaging MAGNETIC RESONANCE IN MEDICINE O'Halloran, R., Aksoy, M., Aboussouan, E., Peterson, E., Van, A., Bammer, R. 2015; 73 (2): 565-576

    Abstract

    Diffusion contrast in diffusion-weighted steady-state free precession magnetic resonance imaging (MRI) is generated through the constructive addition of signal from many coherence pathways. Motion-induced phase causes destructive interference which results in loss of signal magnitude and diffusion contrast. In this work, a three-dimensional (3D) navigator-based real-time correction of the rigid body motion-induced phase errors is developed for diffusion-weighted steady-state free precession MRI.The efficacy of the real-time prospective correction method in preserving phase coherence of the steady state is tested in 3D phantom experiments and 3D scans of healthy human subjects.In nearly all experiments, the signal magnitude in images obtained with proposed prospective correction was higher than the signal magnitude in images obtained with no correction. In the human subjects, the mean magnitude signal in the data was up to 30% higher with prospective motion correction than without. Prospective correction never resulted in a decrease in mean signal magnitude in either the data or in the images.The proposed prospective motion correction method is shown to preserve the phase coherence of the steady state in diffusion-weighted steady-state free precession MRI, thus mitigating signal magnitude losses that would confound the desired diffusion contrast. Magn Reson Med 73:565-576, 2015. © 2014 Wiley Periodicals, Inc.

    View details for DOI 10.1002/mrm.25159

    View details for Web of Science ID 000348139500013

  • Slab Profile Encoding (PEN) for Minimizing Slab Boundary Artifact in Three-Dimensional Diffusion-Weighted Multislab Acquisition MAGNETIC RESONANCE IN MEDICINE Van, A. T., Aksoy, M., Holdsworth, S. J., Kopeinigg, D., Vos, S. B., Bammer, R. 2015; 73 (2): 605-613

    Abstract

    To propose a method for mitigating slab boundary artifacts in three-dimensional (3D) multislab diffusion imaging with no or minimal increases in scan time.The multislab acquisition was treated as parallel imaging acquisition where the slab profiles acted as the traditional receiver sensitivity profiles. All the slabs were then reconstructed simultaneously along the slab direction using Cartesian-based sensitivity encoding (SENSE) reconstruction. The slab profile estimation was performed using either a Bloch simulation or a calibration scan.Both phantom and in vivo results showed negligible slab boundary artifacts after reconstruction using the proposed method. The performance of the proposed method is comparable to the state-of-the-art slab combination method without the scan time penalty that depends on the number of acquired volumes. The obtained g-factor map of the SENSE reconstruction problem showed a maximum g-factor of 1.7 in the region of interest.We proposed a novel method for mitigating slab boundary artifacts in 3D diffusion imaging by treating the multislab acquisition as a parallel imaging acquisition and reconstructing all slabs simultaneously using Cartesian SENSE. Unlike existing methods, the scan time increase, if any, does not scale with the number of image volumes acquired. Magn Reson Med 73:605-613, 2015. © 2014 Wiley Periodicals, Inc.

    View details for DOI 10.1002/mrm.25169

    View details for Web of Science ID 000348139500017

  • Diffusion-Weighted Imaging with Dual-Echo Echo-Planar Imaging for Better Sensitivity to Acute Stroke AMERICAN JOURNAL OF NEURORADIOLOGY Holdsworth, S. J., Yeom, K. W., Antonucci, M. U., Andre, J. B., Rosenberg, J., Aksoy, M., Straka, M., Fischbein, N. J., Bammer, R., Moseley, M. E., Zaharchuk, G., Skare, S. 2014; 35 (7): 1293-1302

    Abstract

    Parallel imaging facilitates the acquisition of echo-planar images with a reduced TE, enabling the incorporation of an additional image at a later TE. Here we investigated the use of a parallel imaging-enhanced dual-echo EPI sequence to improve lesion conspicuity in diffusion-weighted imaging.Parallel imaging-enhanced dual-echo DWI data were acquired in 50 consecutive patients suspected of stroke at 1.5T. The dual-echo acquisition included 2 EPI for 1 diffusion-preparation period (echo 1 [TE = 48 ms] and echo 2 [TE = 105 ms]). Three neuroradiologists independently reviewed the 2 echoes by using the routine DWI of our institution as a reference. Images were graded on lesion conspicuity, diagnostic confidence, and image quality. The apparent diffusion coefficient map from echo 1 was used to validate the presence of acute infarction. Relaxivity maps calculated from the 2 echoes were evaluated for potential complementary information.Echo 1 and 2 DWIs were rated as better than the reference DWI. While echo 1 had better image quality overall, echo 2 was unanimously favored over both echo 1 and the reference DWI for its high sensitivity in detecting acute infarcts.Parallel imaging-enhanced dual-echo diffusion-weighted EPI is a useful method for evaluating lesions with reduced diffusivity. The long TE of echo 2 produced DWIs that exhibited superior lesion conspicuity compared with images acquired at a shorter TE. Echo 1 provided higher SNR ADC maps for specificity to acute infarction. The relaxivity maps may serve to complement information regarding blood products and mineralization.

    View details for DOI 10.3174/ajnr.A3921

    View details for Web of Science ID 000339138200010

  • Prospective motion correction using inductively coupled wireless RF coils MAGNETIC RESONANCE IN MEDICINE Ooi, M. B., Aksoy, M., Maclaren, J., Watkins, R. D., Bammer, R. 2013; 70 (3): 639-647

    View details for DOI 10.1002/mrm.24845

    View details for Web of Science ID 000323543600005

  • 3D isotropic high-resolution diffusion-weighted MRI of the whole brain with a motion-corrected steady-state free precession sequence MAGNETIC RESONANCE IN MEDICINE O'Halloran, R. L., Aksoy, M., Van, A. T., Bammer, R. 2013; 70 (2): 466-478

    Abstract

    The main obstacle to high-resolution (<1.5 mm isotropic) 3D diffusion-weighted MRI is the differential motion-induced phase error from shot-to-shot. In this work, the phase error is addressed with a hybrid 3D navigator approach that corrects motion-induced phase in two ways. In the first, rigid-body motion is corrected for every shot. In the second, repeatable nonrigid-body pulsation is corrected for each portion of the cardiac cycle. These phase error corrections were implemented with a 3D diffusion-weighted steady- state free precession pulse sequence and were shown to mitigate signal dropouts caused by shot-to-shot phase inconsistencies compared to a standard gridding reconstruction in healthy volunteers. The proposed approach resulted in diffusion contrast more similar to the contrast observed in the reference echo-planer imaging scans than reconstruction of the same data without correction. Fractional anisotropy and Color fractional anisotropy maps generated with phase-corrected data were also shown to be more similar to echo-planer imaging reference scans than those generated without phase correction. Magn Reson Med, 2012. © 2012 Wiley Periodicals, Inc.

    View details for DOI 10.1002/mrm.24489

    View details for Web of Science ID 000322128300019

    View details for PubMedID 23042686

  • Prospective optical motion correction for 3D time-of-flight angiography MAGNETIC RESONANCE IN MEDICINE Kopeinigg, D., Aksoy, M., Forman, C., Straka, M., Seaman, D., Rosenberg, J., Fleischmann, D., Hornegger, J., Bammer, R. 2013; 69 (6): 1623-1633

    Abstract

    Magnetic resonance angiograms are often nondiagnostic due to patient motion. In clinical practice, the available time to repeat motion-corrupted scans is very limited-especially in patients who suffer from acute cerebrovascular conditions. Here, the feasibility of an optical motion correction system to prospectively correct patient motion for 3D time-of-flight magnetic resonance angiography was investigated. Experiments were performed on five subjects with and without parallel imaging (SENSE R = 2) on a 1.5 T unit. Two human readers assessed the data and were in good agreement (kappa: 0.77). The results from this study indicate that the optical motion correction system greatly reduces motion artifacts when motion was present and did not impair the image quality in the absence of motion. Statistical analysis showed no significant difference between the (vendor-provided) SENSE and the nonaccelerated acquisitions. In conclusion, the optical motion correction system tested in this study has the potential to greatly improve 3D time-of-flight angiograms regardless of whether it is used with or without SENSE. Magn Reson Med, 2013. © 2012 Wiley Periodicals, Inc.

    View details for DOI 10.1002/mrm.24423

    View details for Web of Science ID 000319074100013

    View details for PubMedID 22887025

  • Combined prospective and retrospective correction to reduce motion-induced image misalignment and geometric distortions in EPI MAGNETIC RESONANCE IN MEDICINE Ooi, M. B., Muraskin, J., Zou, X., Thomas, W. J., Krueger, S., Aksoy, M., Bammer, R., Brown, T. R. 2013; 69 (3): 803-811

    Abstract

    Despite rigid-body realignment to compensate for head motion during an echo-planar imaging time-series scan, nonrigid image deformations remain due to changes in the effective shim within the brain as the head moves through the B(0) field. The current work presents a combined prospective/retrospective solution to reduce both rigid and nonrigid components of this motion-related image misalignment. Prospective rigid-body correction, where the scan-plane orientation is dynamically updated to track with the subject's head, is performed using an active marker setup. Retrospective distortion correction is then applied to unwarp the remaining nonrigid image deformations caused by motion-induced field changes. Distortion correction relative to a reference time-frame does not require any additional field mapping scans or models, but rather uses the phase information from the echo-planar imaging time-series itself. This combined method is applied to compensate echo-planar imaging scans of volunteers performing in-plane and through-plane head motions, resulting in increased image stability beyond what either prospective or retrospective rigid-body correction alone can achieve. The combined method is also assessed in a blood oxygen level dependent functional MRI task, resulting in improved Z-score statistics.

    View details for DOI 10.1002/mrm.24285

    View details for Web of Science ID 000315331300021

    View details for PubMedID 22499027

  • Diffusion tensor imaging (DTI) with retrospective motion correction for large-scale pediatric imaging JOURNAL OF MAGNETIC RESONANCE IMAGING Holdsworth, S. J., Aksoy, M., Newbould, R. D., Yeom, K., Van, A. T., Ooi, M. B., Barnes, P. D., Bammer, R., Skare, S. 2012; 36 (4): 961-971

    Abstract

    To develop and implement a clinical DTI technique suitable for the pediatric setting that retrospectively corrects for large motion without the need for rescanning and/or reacquisition strategies, and to deliver high-quality DTI images (both in the presence and absence of large motion) using procedures that reduce image noise and artifacts.We implemented an in-house built generalized autocalibrating partially parallel acquisitions (GRAPPA)-accelerated diffusion tensor (DT) echo-planar imaging (EPI) sequence at 1.5T and 3T on 1600 patients between 1 month and 18 years old. To reconstruct the data, we developed a fully automated tailored reconstruction software that selects the best GRAPPA and ghost calibration weights; does 3D rigid-body realignment with importance weighting; and employs phase correction and complex averaging to lower Rician noise and reduce phase artifacts. For select cases we investigated the use of an additional volume rejection criterion and b-matrix correction for large motion.The DTI image reconstruction procedures developed here were extremely robust in correcting for motion, failing on only three subjects, while providing the radiologists high-quality data for routine evaluation.This work suggests that, apart from the rare instance of continuous motion throughout the scan, high-quality DTI brain data can be acquired using our proposed integrated sequence and reconstruction that uses a retrospective approach to motion correction. In addition, we demonstrate a substantial improvement in overall image quality by combining phase correction with complex averaging, which reduces the Rician noise that biases noisy data.

    View details for DOI 10.1002/jmri.23710

    View details for Web of Science ID 000308884300022

    View details for PubMedID 22689498

  • Model for the correction of motion-induced phase errors in multishot diffusion-weighted-MRI of the head: Are cardiac-motion-induced phase errors reproducible from beat-to-beat? MAGNETIC RESONANCE IN MEDICINE O'Halloran, R. L., Holdsworth, S., Aksoy, M., Bammer, R. 2012; 68 (2): 430-440

    Abstract

    In diffusion-weighted imaging, multishot acquisitions are problematic due to intershot inconsistencies of the phase caused by motion during the diffusion-encoding gradients. A model for the motion-induced phase errors in diffusion-weighted-MRI of the brain is presented, in which rigid-body and nonrigid-body motion are separated. In the model, it is assumed that nonrigid-body motion is due to cardiac pulsation, and that the motion patterns are repeatable from beat-to-beat. To test the validity of this assumption, the repeatability of nonrigid-body motion-induced phase errors is quantified in three healthy volunteers. Nonrigid-body motion-induced phase was found to significantly correlate (P < 0.05) with pulse-oximeter waveforms in ~83% of the pixels tested across all slices and subjects.

    View details for DOI 10.1002/mrm.23245

    View details for Web of Science ID 000306318900014

    View details for PubMedID 22213138

  • Hybrid prospective and retrospective head motion correction to mitigate cross-calibration errors MAGNETIC RESONANCE IN MEDICINE Aksoy, M., Forman, C., Straka, M., Cukur, T., Hornegger, J., Bammer, R. 2012; 67 (5): 1237-1251

    Abstract

    Utilization of external motion tracking devices is an emerging technology in head motion correction for MRI. However, cross-calibration between the reference frames of the external tracking device and the MRI scanner can be tedious and remains a challenge in practical applications. In this study, we present two hybrid methods, both of which combine prospective, optical-based motion correction with retrospective entropy-based autofocusing to remove residual motion artifacts. Our results revealed that in the presence of cross-calibration errors between the optical tracking device and the MR scanner, application of retrospective correction on prospectively corrected data significantly improves image quality. As a result of this hybrid prospective and retrospective motion correction approach, the requirement for a high-quality calibration scan can be significantly relaxed, even to the extent that it is possible to perform external prospective motion tracking without any prior cross-calibration step if a crude approximation of cross-calibration matrix exists. Moreover, the motion tracking system, which is used to reduce the dimensionality of the autofocusing problem, benefits the retrospective approach at the same time.

    View details for DOI 10.1002/mrm.23101

    View details for Web of Science ID 000302619400005

    View details for PubMedID 21826729

  • Optical motion tracking to improve image quality in MRI of the brain IMAGE RECONSTRUCTION FROM INCOMPLETE DATA VII Maclaren, J., Aksoy, M., Ooi, M., Bammer, R. 2012; 8500

    View details for DOI 10.1117/12.953612

    View details for Web of Science ID 000312165100002

  • Self-encoded marker for optical prospective head motion correction in MRI Forman, C., Aksoy, M., Hornegger, J., Bammer, R. ELSEVIER SCIENCE BV. 2011: 708-719

    Abstract

    The tracking and compensation of patient motion during a magnetic resonance imaging (MRI) acquisition is an unsolved problem. For brain MRI, a promising approach recently suggested is to track the patient using an in-bore camera and a checkerboard marker attached to the patient's forehead. However, the possible tracking range of the head pose is limited by the fact that the locally attached marker must be entirely visible inside the camera's narrow field of view (FOV). To overcome this shortcoming, we developed a novel self-encoded marker where each feature on the pattern is augmented with a 2-D barcode. Hence, the marker can be tracked even if it is not completely visible in the camera image. Furthermore, it offers considerable advantages over the checkerboard marker in terms of processing speed, since it makes the correspondence search of feature points and marker-model coordinates, which are required for the pose estimation, redundant. The motion correction with the novel self-encoded marker recovered a rotation of 18° around the principal axis of the cylindrical phantom in-between two scans. After rigid registration of the resulting volumes, we measured a maximal error of 0.39 mm and 0.15° in translation and rotation, respectively. In in vivo experiments, the motion compensated images in scans with large motion during data acquisition indicate a correlation of 0.982 compared to a corresponding motion-free reference.

    View details for DOI 10.1016/j.media.2011.05.018

    View details for Web of Science ID 000295426200005

    View details for PubMedID 21708477

  • Real-Time Optical Motion Correction for Diffusion Tensor Imaging MAGNETIC RESONANCE IN MEDICINE Aksoy, M., Forman, C., Straka, M., Skare, S., Holdsworth, S., Hornegger, J., Bammer, R. 2011; 66 (2): 366-378

    Abstract

    Head motion is a fundamental problem in brain MRI. The problem is further compounded in diffusion tensor imaging because of long acquisition times, and the sensitivity of the tensor computation to even small misregistration. To combat motion artifacts in diffusion tensor imaging, a novel real-time prospective motion correction method was introduced using an in-bore monovision system. The system consists of a camera mounted on the head coil and a self-encoded checkerboard marker that is attached to the patient's forehead. Our experiments showed that optical prospective motion correction is more effective at removing motion artifacts compared to image-based retrospective motion correction. Statistical analysis revealed a significant improvement in similarity between diffusion data acquired at different time points when prospective correction was used compared to retrospective correction (P<0.001).

    View details for DOI 10.1002/mrm.22787

    View details for Web of Science ID 000293256800008

    View details for PubMedID 21432898

  • Effects of motion and b-matrix correction for high resolution DTI with short-axis PROPELLER-EPI NMR IN BIOMEDICINE Aksoy, M., Skare, S., Holdsworth, S., Bammer, R. 2010; 23 (7): 794-802

    Abstract

    Short-axis PROPELLER-EPI (SAP-EPI) has been proven to be very effective in providing high-resolution diffusion-weighted and diffusion tensor data. The self-navigation capabilities of SAP-EPI allow one to correct for motion, phase errors, and geometric distortion. However, in the presence of patient motion, the change in the effective diffusion- encoding direction (i.e. the b-matrix) between successive PROPELLER 'blades' can decrease the accuracy of the estimated diffusion tensors, which might result in erroneous reconstruction of white matter tracts in the brain. In this study, we investigate the effects of alterations in the b-matrix as a result of patient motion on the example of SAP-EPI DTI and eliminate these effects by incorporating our novel single-step non-linear diffusion tensor estimation scheme into the SAP-EPI post-processing procedure. Our simulations and in-vivo studies showed that, in the presence of patient motion, correcting the b-matrix is necessary in order to get more accurate diffusion tensor and white matter pathway reconstructions.

    View details for DOI 10.1002/nbm.1490

    View details for Web of Science ID 000283014300011

    View details for PubMedID 20222149

  • Self-encoded marker for optical prospective head motion correction in MRI. Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention Forman, C., Aksoy, M., Hornegger, J., Bammer, R. 2010; 13: 259-266

    Abstract

    The tracking and compensation of patient motion during a magnetic resonance imaging (MRI) acqusition is an unsolved problem. For brain MRI, a promising approach recently suggested is to track the patient using an in-bore camera and a checkerboard marker attached to the patient's forehead. However, the possible tracking range of the head pose is limited by the locally attached marker that must be entirely visible inside the camera's narrow field of view (FOV). To overcome this shortcoming, we developed a novel self-encoded marker where each feature on the pattern is augmented with a 2-D barcode. Hence, the marker can be tracked even if it is not completely visible in the camera image. Furthermore, it offers considerable advantages over the checkerboard marker in terms of processing speed, since it makes the correspondence search of feature points and marker-model coordinates, which are required for the pose estimation, redundant. The motion correction with the novel self-encoded marker recovered a rotation of 18 degrees around the principal axis of the cylindrical phantom in-between two scans. After rigid registration of the resulting volumes, we measured a maximal error of 0.39 mm and 0.15 degrees in translation and rotation, respectively. In in-vivo experiments, the motion compensated images in scans with large motion during data acquisition indicate a correlation of 0.982 compared to a corresponding motion-free reference.

    View details for PubMedID 20879239

  • Self-encoded Marker for Optical Prospective Head Motion Correction in MRI MEDICAL IMAGE COMPUTING AND COMPUTER-ASSISTED INTERVENTION - MICCAI 2010, PT I Forman, C., Aksoy, M., Hornegger, J., Bammer, R. 2010; 6361: 259-266
  • Single-step Nonlinear diffusion tensor estimation in the presence of microscopic and macroscopic motion MAGNETIC RESONANCE IN MEDICINE Aksoy, M., Liu, C., Moseley, M. E., Bammer, R. 2008; 59 (5): 1138-1150

    Abstract

    Patient motion can cause serious artifacts in diffusion tensor imaging (DTI), diminishing the reliability of the estimated diffusion tensor information. Studies in this field have so far been limited mainly to the correction of miniscule physiological motion. In order to correct for gross patient motion it is not sufficient to correct for misregistration between successive shots; the change in the diffusion-encoding direction must also be accounted for. This becomes particularly important for multishot sequences, whereby-in the presence of motion-each shot is encoded with a different diffusion weighting. In this study a general mathematical framework to correct for gross patient motion present in a multishot and multicoil DTI scan is presented. A signal model is presented that includes the effect of rotational and translational motion in the patient frame of reference. This model was used to create a nonlinear least-squares formulation, from which the diffusion tensors were obtained using a nonlinear conjugate gradient algorithm. Applications to both phantom simulations and in vivo studies showed that in the case of gross motion the proposed algorithm performs superiorly compared to conventional methods used for tensor estimation.

    View details for DOI 10.1002/mrm.21558

    View details for Web of Science ID 000255230700024

    View details for PubMedID 18429035

  • Time-resolved 3D quantitative flow MRI of the major intracranial vessels: Initial experience and comparative evaluation at 1.5T and 3.0T in combination with parallel imaging MAGNETIC RESONANCE IN MEDICINE Bammer, R., Hope, T. A., Aksoy, M., Alley, M. T. 2007; 57 (1): 127-140

    Abstract

    Exact knowledge of blood flow characteristics in the major cerebral vessels is of great relevance for diagnosing cerebrovascular abnormalities. This involves the assessment of hemodynamically critical areas as well as the derivation of biomechanical parameters such as wall shear stress and pressure gradients. A time-resolved, 3D phase-contrast (PC) MRI method using parallel imaging was implemented to measure blood flow in three dimensions at multiple instances over the cardiac cycle. The 4D velocity data obtained from 14 healthy volunteers were used to investigate dynamic blood flow with the use of multiplanar reformatting, 3D streamlines, and 4D particle tracing. In addition, the effects of magnetic field strength, parallel imaging, and temporal resolution on the data were investigated in a comparative evaluation at 1.5T and 3T using three different parallel imaging reduction factors and three different temporal resolutions in eight of the 14 subjects. Studies were consistently performed faster at 3T than at 1.5T because of better parallel imaging performance. A high temporal resolution (65 ms) was required to follow dynamic processes in the intracranial vessels. The 4D flow measurements provided a high degree of vascular conspicuity. Time-resolved streamline analysis provided features that have not been reported previously for the intracranial vasculature.

    View details for DOI 10.1002/mrm.21109

    View details for Web of Science ID 000243538900015

    View details for PubMedID 17195166

  • Augmented generalized SENSE reconstruction to correct for rigid body motion MAGNETIC RESONANCE IN MEDICINE Bammer, R., Aksoy, M., Liu, C. 2007; 57 (1): 90-102

    Abstract

    The correction of motion artifacts continues to be a significant problem in MRI. In the case of uncooperative patients, such as children, or patients who are unable to remain stationary, the accurate determination and correction of motion artifacts becomes a very important prerequisite for achieving good image quality. The application of conventional motion-correction strategies often produces inconsistencies in k-space data. As a result, significant residual artifacts can persist. In this work a formalism is introduced for parallel imaging in the presence of motion. The proposed method can improve overall image quality because it diminishes k-space inconsistencies by exploiting the complementary image encoding capacity of individual receiver coils. Specifically, an augmented version of an iterative SENSE reconstruction is used as a means of synthesizing the missing data in k-space. Motion is determined from low-resolution navigator images that are coregistered by an automatic registration routine. Navigator data can be derived from self-navigating k-space trajectories or in combination with other navigation schemes that estimate patient motion. This correction method is demonstrated by interleaved spiral images collected from volunteers. Conventional spiral scans and scans corrected with proposed techniques are shown, and the results illustrate the capacity of this new correction approach.

    View details for DOI 10.1002/mrm.21106

    View details for Web of Science ID 000243538900012

    View details for PubMedID 17191225